ArticlePeerJ2019
LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics.
Article in PeerJ, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Amplification bias in sequencing-based spatial transcriptomics: sources, mechanisms, impacts, and mitigation strategies.Briefings in bioinformatics · 2026Review
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- Ceg1 depletion reveals mechanisms governing degradation of non-capped RNAs in Saccharomyces cerevisiae.Communications biology · 2023Article
- CYP19A1 mediates severe SARS-CoV-2 disease outcome in males.Cell reports. Medicine · 2023Article
- Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics.Bioinformatics (Oxford, England) · 2023Article
- RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice.BMC plant biology · 2023Article
- Comprehensive Transcriptomic Analysis of Novel Class I HDAC Proteolysis Targeting Chimeras (PROTACs).Biochemistry · 2023Article
- Non-coding RNAs associated with Prader-Willi syndrome regulate transcription of neurodevelopmental genes in human induced pluripotent stem cells.Human molecular genetics · 2023Article
- Hypoxia Inhibits Subretinal Inflammation Resolution Thrombospondin-1 Dependently.International journal of molecular sciences · 2022Article
- Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision.Briefings in bioinformatics · 2021Article
- Accelerated aging of the brain transcriptome by the common chemotherapeutic doxorubicin.Experimental gerontology · 2021Article
- Article
- Systemic and adipocyte transcriptional and metabolic dysregulation in idiopathic intracranial hypertension.JCI insight · 2021Article
- Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis.PLoS pathogens · 2021Article
- 3Genome biology · 2021Article
- Regulation of Cell Type-Specific Immunity Networks in Arabidopsis Roots.The Plant cell · 2020Article
- Article
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3 authors.
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Abstract
Protocols for preparing RNA sequencing (RNA-seq) libraries, most prominently "Smart-seq" variations, introduce global biases that can have a significant impact on the quantification of gene expression levels. This global bias can lead to drastic over- or under-representation of RNA in non-linear length-dependent fashion due to enzymatic reactions during cDNA production. It is currently not corrected by any RNA-seq software, which mostly focus on local bias in coverage along RNAs. This paper describes LiBiNorm, a simple command line program that mimics the popular htseq-count software and allows diagnostics, quantification, and global bias removal. LiBiNorm outputs gene expression data that has been normalized to correct for global bias introduced by the Smart-seq2 protocol. In addition, it produces data and several plots that allow insights into the experimental history underlying library preparation. The LiBiNorm package includes an R script that allows visualization of the main results. LiBiNorm is the first software application to correct for the global bias that is introduced by the Smart-seq2 protocol. It is freely downloadable at http://www2.warwick.ac.uk/fac/sci/lifesci/research/libinorm.
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